Most currently available data backup tools don't have the capability to backup data storage volumes that reside on virtual disks along with related or counterpart data storage volumes that reside on physical disks in a synchronized manner. That is, most data backup tools use two different mechanisms, one to backup data from the virtual volumes and another to backup data from the physical volumes, respectively.
In other words, the backup (e.g., snapshot) operations performed on the virtual volumes and the physical volumes are performed in two separate operations. This means that the backup copies will not be consistent (i.e., not copied at the exact same point in time) because the currently available backup mechanisms are unable to synchronously perform the snapshot operations on both the virtual volumes and the physical volumes at the same time.
For example, consider a scenario where mapped drives C:\ and D:\ reside on virtual disks and drive E:\ on a physical disk. If a SQL application is installed on drive C:\ the SQL database on drive D:\ and the related SQL logs on drive E:\ then the backups performed on the volumes across the virtual and physical domains would not be synchronized.